chrX-154706415-CAAAA-C

Variant names:

• chrX-154706415-CAAAA-C
• rs35975601
• NM_001081573.3:c.1069+5810_1069+5813delTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001081573.3(GAB3):​c.1069+5810_1069+5813delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., 0 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: GAB3 NM_001081573.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 0 publications found

Genes affected

GAB3 (HGNC:17515): (GRB2 associated binding protein 3) This gene is a member of the GRB2-associated binding protein gene family. These proteins are scaffolding/docking proteins that are involved in several growth factor and cytokine signaling pathways, and they contain a pleckstrin homology domain, and bind SHP2 tyrosine phosphatase and GRB2 adapter protein. The protein encoded by this gene facilitates macrophage differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001081573.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAB3	NM_001081573.3	MANE Select	c.1069+5810_1069+5813delTTTT		intron	N/A	NP_001075042.1	Q8WWW8-2
	GAB3	NM_080612.4		c.1066+5810_1066+5813delTTTT		intron	N/A	NP_542179.1	Q8WWW8-1
	GAB3	NM_001282283.2		c.1069+5810_1069+5813delTTTT		intron	N/A	NP_001269212.1	Q8WWW8-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAB3	ENST00000424127.3	TSL:1 MANE Select	c.1069+5810_1069+5813delTTTT		intron	N/A	ENSP00000399588.2	Q8WWW8-2
	GAB3	ENST00000369575.7	TSL:1	c.1066+5810_1066+5813delTTTT		intron	N/A	ENSP00000358588.3	Q8WWW8-1
	GAB3	ENST00000496390.5	TSL:1	n.617-6360_617-6357delTTTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 93552 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 93552 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20596

African (AFR) AF: 0.00 AC: 0 AN: 24733

American (AMR) AF: 0.00 AC: 0 AN: 8550

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2386

East Asian (EAS) AF: 0.00 AC: 0 AN: 3045

South Asian (SAS) AF: 0.00 AC: 0 AN: 2014

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3433

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 205

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 47348

Other (OTH) AF: 0.00 AC: 0 AN: 1235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs35975601; hg19: chrX-153934690;